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Allison Marie Burns
PhD, Bioinformatician and Genomicist
I am a bioinformatician and scientist with more than 8 years of experience working with NGS datasets. I am passionate about using multi-omics approaches to explore the genetics of diseases and to develop novel therapeutics to ameliorate those disorders. My motivation is to leverage my skills as part of a team to successfully conduct and communicate data-drive research.
Experience
Doctoral Researcher and Bioinformatician
Laboratory of Neuroepigenetics - Gräff Lab
EPFL
2022 - 2016
- Integrated multi-omics datasets to determine mechanisms of HDACi treatment in memory amelioration
- Designed, performed and analyzed molecular and bioinformatic experiments
- Created and managed analysis pipelines for myself and colleagues
- Advised colleagues on best methods for NGS sample and library preparation
- Maintained and organized computational storage needs for the lab
Bioinformatician / Research Associate
Baumann Laboratory
Stowers Institute for Medical Research
2016 - 2013
- Analyzed RNA-seq data and performed transcriptome assembly with Trinity
- Performed basic tissue culture and molecular experiments
Undergraduate Researcher
Bradshaw-Holzapfel Laboratory
University of Oregon
2012 - 2010
- Measured animal fitness in extreme light environments
- Studied the evolutionary divergence of circadian clock genes in mosquitos
Education
Ph.D. in Neuroscience
Lausanne, Switzerland
École Polytechnique Fédérale de Lausanne
2022
Title: Epigenetic memory aids: Synaptic and molecular effects of HDAC
inhibition that support memory formation
M.Sc. in Bioinformatics
Eugene, Oregon, USA
University of Oregon
2013
Title: Effects of the splicing inhibitor, Isoginkgetin, on human Telomerase RNA
B.Sc. in Biology
Eugene, Oregon, USA
University of Oregon
2012
Project: Evolutionary genetics of geographical variation, seasonal development and circadian timing in the North American mosquito species, Wyeomyia smithii
Technical Skills
Bioinformatics and NGS Data Analysis
- R/Bioconductor (highly proficient), Bash (proficient), Python (competent)
- Data wrangling, statistical analysis, and data visualization in R (tidyr, dplyr, ggplot, etc)
- Quality control and processing of sequencing data (FastQC, STAR alignment, Bowtie suite, CellRanger, etc)
- Analysis and integration of RNA-seq (edgeR, DESeq2), scRNA-seq (Seurat, RNAvelocity) and ChIP-seq (DiffBind)
- Exploration and interpretation of complex omics datasets (BiomaRt, Gprofiler2,TopGO, Cytoscape, etc)
- Ability to link transcription and epigenetic data analysis to behavioral phenotypes
N/A
Computing Experience
- Version control with git and Github
- Software download and maintenance (conda, homebrew, etc)
- Experience using cloud computing and high performance clusters for analysis and storage of large datasets
N/A
Communication
- Documentation with Rmarkdown (Pagedown and KnitR), Emacs Org Mode and Jupyter Notebooks
- Presenting and communication (Microsoft Office and Adobe Suite) with scientists in my field and unrelated fields
- Excellent written communication in the form of manuscript and thesis writing
- Website development (R Blogdown and Wordpress with basic markdown and HTML)
N/A
Laboratory Techniques
- Techniques for NGS experimentation (nuclear and RNA extractions, ChIP, library preparation, etc)
- Molecular Biology Techniques (FANS, Western, qPCR, etc)
- Animal Handling (mouse and insect)
N/A
Courses and Training
Genome variant analysis
Swiss Institute of Bioinformatics
N/A
2022
Scientific writing for biomedical articles
École Polytechnique Fédérale de Lausanne
N/A
2021
Advanced topics in single-cell transcriptomics
Swiss Institute of Bioinformatics
N/A
2020
Genetic and epigenetic mechanisms underlying brain disorders
FENS-Hertie Winter School 2019
N/A
2019
Science and Engineering Teaching and Learning
CAPE-Teaching Support Centre, EPFL
N/A
2018
Image Processing for Life Scientists
École Polytechnique Fédérale de Lausanne
N/A
2016
High Performance Computing (HPC) in Life Sciences
Swiss Institute of Bioinformatics
N/A
2016
Teaching and Mentoring
Robust data analysis: an introduction to R
Designed and taught introduction to R in an afternoon lecture
Open Science in Practice Summer School
2019
Project Supervisor for Bachelor Students
Mentored students for projects (3wks - 1yr) involving lab techniques and bioinformatic analysis
EPFL
2017-21
Laboratoire Intégré en Sciences de la Vie I/II
Taught and demonstrated lab techniques and analysis to first year bachelor students
EPFL
2017-19
Selected Presentations
Federation of European Neuroscience Society Forum 2020 (virtual poster)
Testing the theory of Epigenetic Priming in Fear Memory Conditioning
Glasgow, Scotland
2020
FENS-Hertie Winter School 2019 (poster)
Testing the theory of Epigenetic Priming in Fear Memory Conditioning
Obergurgl, Austria
2019
Society For Neuroscience Annual Meeting 2019 (poster)
Testing the theory of Epigenetic Priming in Fear Memory Conditioning
Chicago, Illinois, USA
2019
Molecular and Cellular Cognition Society 18th Annual Meeting (talk)
Testing the theory of Epigenetic Priming in Fear Memory Conditioning
Chicago, Illinois, USA
2019
Single Cell Biology Symposium (talk)
Variations of epigenetic priming across hippocampal cell types during memory formation
Lausanne, Switzerland
2019
Lemanic Neuroscience Annual Meeting (poster)
Testing the theory of Epigenetic Priming in Fear Memory Conditioning
Diableret, Switzerland
2019
Neural Circuits and Behavior (talk)
HDAC inhibitors that prime in fear memory conditioning
Lausanne, Switzerland
2018
Federation of European Neuroscience Society Forum 2018 (poster)
Epigenetic Priming and Fear Memory Conditioning
Berlin, Germany
2018
Functional Genomics Symposium (talk)
Epigenetic priming in fear memory conditioning
Lausanne, Switzerland
2018
Publications
The HDACi inhibitor CI-994 acts as a molecular memory aid by enhancing synaptic and intra-cellular communication after learning
Allison M. Burns, Mélissa Farinelli-Scharly, Sandrine Hugues-Ascery, Jose Vicente Sanchez-Mut, Giulia Santoni,Johannes Gräff
BioRxiv
N/A
2021
A thalamo-amygdalar circuit underlying the extinction of remote fear memories
Bianca A. Silva, Simone Astori, Allison M. Burns, Hedrik Heiser, Lukas van den Heuvel, Giulia Santoni,
Maria Fernanda Martinez-Reza, Carmen Sandi, Johannes Gräff
Nature Neuroscience
N/A
2021
Cognitive epigenetic priming: Leveraging histone acetylation for memory amelioration
Allison M. Burns, Johannes Gräff
Current Opinion in Neurobiology
N/A
2020
A cFos activation map of remote fear memory attenuation
Bianca A. Silva, Allison M. Burns, Johannes Gräff
Psychopharmacology
N/A
2018
Human Telomerase RNA Processing and Quality Control
Chi-Kang Tseng, Hui-Fang Wang, Allison M. Burns, Morgan R. Schroeder, Martina Gaspari, Peter Baumann
Cell Reports
N/A
2015
Leadership and Outreach
EDNE Neuroscience Student Association
Event Organizer
N/A
2019
R-Ladies Lausanne
Member
N/A
2018-21
Letters to a Pre-scientist
STEM Professional
N/A
2018-21
Association of Doctoral Students in Life Sciences (ADSV)
Webmaster & Head of Coaches
N/A
2018-20